Technologically Advanced Shinobi
by helpusobi1kenobi
Summary: What will happen to the Elemental Nations, when it is revealed that the Kyuubi Jinchuriki- one Naruto Uzumaki Namikaze has power, knowledge and technologies not of their dimension. A Naruto who has a prototype Motherbox fused into him, which gives him the powers of several New Gods and unbelievable power. Harem fic. God-like Naruto.
1. Chapter 1: Falling Stars

Technologically Advanced Shinobi: A Naruto fanfic

 **This will be a Harem fic and I would like to Thank HandAssasinSpider-man, Diablo Ex Machina** , **VFSNAKE** , **WraithRune, MadHat886 and RebukeX7**

 **The Original story was written by** **WraithRune.** **I will be reposting his/her story with a few changes until the original story is finished, then I will try to continue with the story and I hope it will be good as the original considering the direction I want to go.**

 **This reality in which I am writing about is taking place in a parallel universe to the Original Naruto-verse. There are many changes in the continuity and the characters, one prominent change is that this universe is connected to the Source from the DC Reality.**

 **Naruto is red haired and violet eyed, the genetic opposite of his canon self. Which means he has a delicate facial structure that makes him look handsome. Guess which red haired hero from DC I am basing Naruto upon?**

 **Here is the new story and WARNING** **THIS STORY WILL HAVE:**

 **FOUL LANGUAGE AND CURSE WORDS.**

 **SEXUAL THEMES THAT SOME WILL FIND DEGRADING AND/OR INSULTING LIKE SHOTACON AND POSSIBLE INCEST. DO NOT READ IF YOU FIND IT INSULTING.**

 **THERE WILL BE REASONABLE AMOUNT OF BASHING AND THIS IS MOSTLY A NARUTO-CENTRIC FIC. ALL CHARACTERS EXCEPT ROMANTIC INTERESTS ARE SECONDARY CHARACTERS.**

 **POSSIBLE BAD GRAMMAR, ADULT THEMES, FAMILIAR CHARACTERS ACTING OUT OF CHARACTER AND MARY SUE.**

 **I DONT OWN THE RIGHTS TO ANY MANGA, ANIME, MARVEL, DC, VIDEO GAMES AND/OR ANIMES! ALSO NO REVIEWS OR REQUESTS.**

 **Any OC's mentioned are my own creation and property.**

 **Review in your free time and all flames will be deleted and ignored. I won't be answering questions just yet.**

 **Chapter One: The Fallen Star**

 **(Universe 9419)**

Pilot: "The military cruiser has been destroyed." (cries frantically) as the small cargo ship warmed up its boom tube tech in preparation for them to escape.

Scientist: "Damm… those **Paradeamons**! We can't let the prototype **Motherbox** fall into their hands." (curses) " **New Genesis** should have sent us more than one cruiser as our escort, now it's too late."

Pilot: "15 seconds to **boom tube** activation." (pale faced as he stared at the screen) "The **Paradeamons** are turning towards us!"

Scientist: "Hurry!"

Ship A.I: "10, 5, 2."

Pilot: "It's activated." (The pilot cried in relief as the cargo ship entered the **Boom Tube**.)

An explosion rocked the ship as a laser blast from one of the pirate ship slammed into the back of the ship just as it disappeared into warp.

Pilot: "Losing **Boom Tube** integrity. We will be dropping out of it in 10 seconds." (says haggardly as he watched the reading output on screen.) "The cargo doors has been blasted open, the **Motherbox** has already falling out of warp into space."

Scientist: "That doesn't matter. I still have the research data. Prepare for another warp immediately after we exited into space." (Orders)

A few light years away, in between space and time, a metallic box drifted aimlessly. It resembled a large thick green metallic brick with a different design and glowing circles in its. It would have stayed there drifting aimlessly within that area in sub space, however a portal opened up and soon the object drifted into the swirling portal and then disappeared not just from the subspace but also from this reality.

(Elsewhere-Another Dimension)

The Yondaime Hokage had just battled Uchiha Madara, freed the Kyuubi from the man's control, and called forth the Shinigami to seal the fox within his own son. Something he had no intention of doing when Kushina's pregnancy hit its apex and the seal holding the Kyuubi weakening to the point where the fox _might_ break free. Minato didn't know _how_ Madara was alive, much less _how_ he knew where Kushina's hideout was during the last few hours of the pregnancy prior to his interventions, but the man had just about screwed up everything for the Hokage, and his village.

Now here he was using his own sealing methods, which were in truth second best when compared to his wife's own, which would bind the fox to his son, and turning Naruto into a Jinchuriki. Minato was not naïve to believe the village would see his son like the hero he wanted the boy to be, as Jinchuriki were hated for what they held, ironically by the very people that made them Jinchuriki in the first place, and yet the Hokage did not want this for his son. The original plan was for Naruto to receive Kyuubi like his wife did at a much older time when Kushina herself could not hold the fox and let the woman use her own sealing methods to transfer the nine-tails to Naruto.

But not everything goes according to plan.

 ** _"Its time mortal. Say goodbye. I have things to do,"_** said the Shinigami, as he saw the blonde man put his son down on the ground, the sealing finally complete, and wished there was some way the boy could be protected from such a harsh life.

Strange how during the entire fight with the fox after Madara fled, as Minato summoned the Death God, no one saw a metallic object fall from the sky from a portal created around the time the spiritual entity was summoned, and land right on the Kyuubi's back. Like a tiny flea amongst its fur, but barely felt by the large mass of demonic chakra, and was sealed into Naruto too.

Minato: Goodbye son. I'm sorry for this. I never wanted this for you. Same with your Mother. Whatever you may think of us in the future, I will understand, and won't hate you for hating me if the village does what I think they will. All I can ask of you is to endure what they dish out and knowing your Mother she'd tell you to return it back a thousand fold.

With that being said, the Shinigami took the soul of Namikaze Minato, but before leaving for its own real, the Death God looked back at Naruto, and sensed something else upon its entry to this realm had happened. Something about the boy's energy had suddenly changed, but was restrained by the seal with his mark, and even in part by the fox itself. The Shinigami could only conclude that whatever this _something_ was, it was not part of the boy, not connected to Kyuubi, and not connected to this very dimension. The Death God had always been told by the other powers above that such a contract was dangerous to have since it tore partially into the dimensional fabric, risking something from another place, from another dimension from getting through, and entering this dimension.

Now it was starting to suspect Kami and Yami were right. Of course...they were _always_ right when it came to matters like that since they had help the Death God make such a contract with the mortals of this village. In the name of balance they said. Needed to be put in place to counter a Forbidden Jutsu that cheated the Shinigami out of a few of the souls in his deathly realm from _staying_ there for an unknown amount of time.

However, the Shinigami could not remove this unknown entity from the boy, as it would mean removing the seal, and freeing the Kyuubi _again_! The Shinigami didn't want that, as it had enough paperwork on its hands already just from the sealing alone, and didn't want to make things even more complicated then it already was.

Let the mortals deal with this situation and if it bit them in the ass? Oh well. More souls for its realm.

Meanwhile on the ground,

Medic-nin: Kushina-sama is alive, Sandaime-sama!

Hiruzen: Get her to the medics, NOW! I will take Naruto myself!

The consequences of this day's events would be beyond comprehension.

 **Six Years Later, Konoha, Forest of Death**

Lying down, bleeding and unconscious on the forest floor was a small Red haired boy with whisker marks on his face. This boy was Naruto Uzumaki Namikaze the son of the Yondiame Hokage Minato Namikaze and Kushina Uzumaki, the third Jinchuriki of the Kyuubi and pariah of Konohagakure. Today is October 10th, the sixth anniversary of the Kyuubi's defeat and Naruto's birthday.

Today was also the day Naruto was once again attacked vicously by an angry mob. He was beaten to an inch of his life.

Fearing reprisal from the Sandiame Hokage, the mob decided to dump his body in a place where his chances of survival would be nonexistent: Training ground 44 aka the forest of death.

Now the innocent child lies on the ground barely hanging on to his life. He had long fallen into unconsciousness due to the pain of his injuries. It seemed all hope was lost and that now the boy would meet his premature death.

Until…something deep within him awakened after years of slumber.

Immediately a glow came over Naruto and soon his injuries seemingly faded away. The blood leaking from the cuts disappeared.

Static filled his head before Naruto felt his head cleared.

 _"… Synchronising with host brain complete. Healing of host body in progress… Extracting host name from memories…_

 _Naruto Uzumaki, I am prototype Motherbox designation Bekka, successfully bound to your brain waves and patterns._

 _Advise to Naruto Uzumaki, you need to find your way out of this forest as a number of primitive hostile lifeforms are near you._

Naruto soon awoke. He looked down to see he was not hurting anymore and that all his bruises were gone. Naruto found to his embarrassment that his clothes were torn off, leaving him completely naked.

 _"Host is embarrassed about nakedness."_ said Bekka in Naruto's head. _"Do you wish me to Matter reassemble your clothes over your body?"_

Naruto: What's a matta riasemble?

He looked around in amazement, he had a feeling that new voice was in his head. He didn't know what I was but it was helping him when no one else did, so he trusted the voice, plus she sounded very kind and friendly for some reason…like a mother.

 _"Matter Reassemble is simply controlling the matter and molecular strutures to create or manifest new objects. I have the ability to reassemble matter within a fixed radius."_ Bekka remarked. _"Would you like me to recreate your clothes that you were wearing?"_

Naruto: Er…(not understanding at all and looking confused) Ok?

 _"Beginning Matter reassembly of last image of Naruto Uzumaki's clothes."_ Bekka said.

Naruto cried out in surprise as a shimmer of light washed over his body. The clothes he was wearing before he was burnt by the fireball reappeared. Naruto reached out and feel the soft fibers in awe.

Naruto: That's… (Naruto began but was cut off as a black shadow landed beside him)

Cat ANBU: Naruto, are you hurt? (asks worriedly as she checked over Naruto)

Naruto: Cat Anbu-san! (delighted) I make a new friend!

Cat ANBU: Good, good. (says distantly as She looked around)

Several more figures appeared from the forest, one of them was the gate guards that had stopped the mob just now.

Cat ANBU: Iruka, who is watching the gates now?

Iruka: The second shift started just as the mob reached. I remembered Naruto was running in this direction so…(cut off by a nod from the anbu)

Cat ANBU: I need you to take Naruto home. The rest of the Anbu and I will need to check out the places where these fireballs fell.

Iruka nodded, quickly bundling up Naruto in his arms and began running towards the village.

Iruka: Go to sleep Naruto.

Iruka said kindly as he took the bundled up boy home.

Naruto opened his mouth to speak but felt the heavy weight of the events of the night washed over him dragging him to unconsciousness.

 **The Next day**

 _"Analyses complete_." The bracelet said on the second day as Naruto went to one of the training grounds by himself. Even at this age, he knew that none of the children's parents would allow them to play with him.

Naruto: What do you mean bekka-san?

 _"It appears that I've landed on an underdeveloped planet."_ Bekka said. _"According to the laws made by the Highfather, I am forbidden to reveal myself to any members from Undeveloped Planets. Unfortunately I've already given you the knowledge of advanced civilization. By my reasoning, that means you are now officially an ally of New Genesis and are answerable to the Highfather."_

Naruto: Huh? (Confused)

 _"It means that you must never reveal my existence to any member of your planet."_ Bekka said patiently. _"Until a way for us to return to New Genesis shows itself, you must keep my existence a secret. I am also assigning administrator rights to only you and ban all access of my usage to others not of New Genesis If anyone else tries to access me they will be dealt with accordingly."_

Naruto: So you'll be my secret friend? (Excited)

 _"You could say that."_ answered Bekka.

Naruto: Bekka! You're my second best friend! (Naruto shouts happily as he began dancing around) "Old man Hokage is my first best friend!"

 _"Since you are an Underdeveloped Planet citizen that came into knowledge of New Genesis, I will begin training you in the basic math and science of New Genesis."_ Bekka said ignoring Naruto's happy shouts.

Naruto: You can do that? (amazed) Be my teacher?

 _"I am a Motherbox, which means that my connection with the source gives me the powers of Omniscience, Omni-Knowledge and Knowledge sharing."_ Bekka explained. _"I will be able to share any knowledge you wish to know about as well as coach you in understanding it."_

Naruto: Cool! When do we start? (asks happily)

The new theories that Bekka taught Naruto had been difficult for his little head to absorb. But he had wanted to impress his new friend and had strived to learn as much as he could, always persevering and cramming the new knowledge in his head. The next half a year had passed quickly as Naruto absorbed what Bekka taught him, he was also able to hold up under the villagers' glares much better since Bekka was constantly there to support him.

Bekka's sensors which could also detect hostile intent also saved Naruto from the villagers pursing him several time. Naruto began to gain a reputation as being uncannily fast and hard to catch.

Naruto began to understand that the New Genesis is another planet….home to the new gods beings of unimaginable power who could do amazing miracles like travel through space and visit other worlds, teleport from one place to another instantaneously, incredible strength and even the power to resurrect the dead.

Bekka's mental communication had been useful in relating images of the various planets, starships and technologies New Genesis had possessed to him. Naruto also realized that Bekka was actually a living computer called a Motherbox, part alive and part highly advanced thinking machine. She even explained who the Highfather was, his enemy Darksied, The social structure of New Genesis and Apokolips and how she was originally made using the powers of the Mobius chair and contained knowledge, powers and skills of: Scott Free aka Miracle man, Orion the son of Darksied, Drax aka Infinity-man, Bekka the goddess of Love and her namesake, Big Barda former member of the furies and Lightray of the Council of Eight. Giving her the power to replicate the powers of several new gods.

She was made with several functions, not including the basic functions all motherboxes have. Unlike the others, she was built with an inbuilt warmind, ability to tap into the quantum force and to use the Alpha and Omega Effects. She was the pinnacle in New God technology and as such she was kept secret until she was supposed to be used in the next conflict against Apokolips.

Of course when he had asked how she had gotten inside his head, to which she told him that it also confused her. She said that she would be running her own investigations as to how it was possible and that she would get back to him on that..

Naruto's world had been opened up by the marvels that Bekka had shown him and Naruto had vowed to understand more of this alien science so that he could build those technologies for himself.

++++++++++++++++  
 **Hokage's Office**

Naruto: Ne jij…Do ou want to go out for some ramen?

Hiruzen: Sorry Naruto, but I have work to do (points to the massive paperwork) But it's a good thing you're here. I was planning to ask you if you'll like to attend the Academy earlier. It might fill up your time with something practical to do.

Naruto: The Academy? Where they teach you how to be a ninja and stuff? (excitedly)

Hiruzen: Yes Naruto. (smiles fondly at Naruto) Remember your promise to be a Hokage one day?

Naruto: Oh that, I can do that no problem now, I have a new dream. (says dismissively)

Hiruzen: Really, and what's that? (asks with interest)

Naruto: I want to travel to the stars. (says with a grin)

The ninja academy was one of the worse experiences of Naruto's life. Three months into the academy and Naruto realized that the teachers were deliberately going out of their way to fail him in his tests and making life hell for him. His ninja studies were stumped, or would have been stumped if not for Bekka.

Due to Bekka's Omni-knowledge and Knowledge-Sharing, she managed to download all the knowledge pertaining to Ninshu and the ways of the Shinobi. She managed to download not only the knowledge from the instructors and all the knowledge from the shinobi library, but also from clan libraries which were forbidden to outsiders.

With all these knowledge, Bekka had begun work to organize the archive of ninja information based on their difficulty level and began to use the huge book knowledge it contained to teach Naruto in the ninja arts. Naruto had also asked her to download the knowledge from all the Hokages and powerful shinobi in the village, both living and dead. Sure, his dream was to travel the stars now, but he had seen all those awesome techniques the Hokage and the ninjas could perform and he wanted to learn everything he could about them.

The first time he showed off his fireball technique at the academy, the teachers had sternly asked him where he stole the technique from. When Naruto was not able to reply, since the book from which the technique came from was from the restricted section of the library, they had put him in detention for a week and reported him to the Hokage.

Naruto had to make up a lie about how he copied a scroll dropped by a ninja and learnt the technique from there. The Hokage had luckily nodded in understanding and cautioned him against trying such a dangerous technique again.

From then on, Naruto learnt to hide his true skills and showed only a poor grade at school. He quickly found that the teachers had been delighted at seeing him do poorly and cause less trouble for him this way. Naruto began to wonder why he was treated with such hatred.

The vast amount of knowledge that Bekka was teaching him had caused him to mature more quickly than those his age, but it had also made him quieter in class and reserved by nature. It allowed him to endure those feelings of hurt about how the others treated him better than how he might have done without Bekka around.

 _"I have isolated the problem for your inability to create a clone technique."_ Bekka supplied in one of their training section. _"From the energy readings I took of you while you did the technique and compared it to those who had done it successfully. It seemed your inability to control your chakra energy is causing the problem. You would do well in techniques that require you to use a large amount of chakra, like the fire breathing technique, but you'll do poorly at those that require finer control and smaller amounts of chakra. I have taken several chakra control exercises and will begin to teach them to you. In time you could possibly through practice be able to use jutsus that need extreme chakra control like medical ninjutsus, genjutsus and even chakra threads on your own. But for now my powers in life transference, telepathy, energy manipulation and Omni-knowledge will make up for that"_

Naruto: Thanks Bekka! (Says with a grin) You know, I've been going through the data about the use of Runes. I seemed to remember seeing some books on the basics of seal making in the library, are they similar?

 _"In a way yes. The way that they were applied in your world however is different. Runes are used in the Federation is more focused on instant results, used in offensive and defensive purposes. The seal making on your planet however requires laborious amounts of seals to complete one powerful task, they are also mostly used for sealing objects and containment."_ Bekka stated. _"I've looked through your schedule. If you sleep one hour less every day, I will be able to teach you the basics of Runes and sealing."_

Naruto: Great Bekka! Thank you! Actually I was thinking of telling the Hokage that I want to quit school for this year and resume the studies when a year later. I plan to use the excuse of wanting to be in the same class as my age group to get him to agreed.

" _Based on the Hokage's cordial treatment of you, your plan has a probability of 90% success._ " Bekka provided helpfully. " _It would also allow me more time to train you in more useful knowledge."_

Naruto: Then I'll find the old man now and tell him. (Says excitedly)

He got to his feet, making his way to the Hokage tower.

+++++++++++++++++++++  
 _One Year Later_

Sarutobi was worried. Naruto had seldom sought him out for the past year after he had requested to quit school and resume his schooling with his age group a year later. At first, the ANBU had reported that Naruto had begun using his time training in the training fields daily. Concerned, Sarutobi had used his telescope technique to find out what Naruto was doing. He had been shocked at finding Naruto using techniques that he should have no knowledge of.

Careful questioning of the boy had revealed that he had slipped in the restricted section of the library a few times and memorized some of the techniques contained in the scrolls. After the warning from Sarutobi of not practicing those techniques until he was older, Naruto had filled his daily life by staying at home or doing basic sparring on a training dummy out in the training fields. From what he observed, other than the times when Naruto had to walk through the village, he basically had no contact with other people.

Sarutobi had tried to meet up weekly with Naruto for ramen which used to be his favorite. Oh, Naruto still visit the Ichiraku Ramen Bar once a week, but he had heard from Teuchi, the ramen bar owner, that Naruto had requested Teuchi to help buy his weekly grocery for him in exchange for a huge tip.

Naruto had confined in the ramen bar owner of how he was always over-charged when he bought the groceries and only receive the poorest quality of the products. Teuchi had muttered angrily about the way that most of the villagers had treated Naruto whom he had always considered as one of the most polite child he had ever seen.

Sarutobi had been touched that Naruto had another friend in the ramen bar owner, and had been even more surprise when he had spied on Naruto whipping up dish after dish of nutritious meals in his small apartment kitchen. Naruto had also abandoned his untidy habits and had even begun keeping his small apartment tidy much to the discomfort of Sarutobi who had known the child for so long.

Naruto had seemed changed after he first started the ninja academy. Sarutobi could only hope that Naruto could get along better with peers his age as he began ninja school tomorrow.

Naruto: Is the old man spying on me again?

Naruto asked as he carefully traced the symbol for Healing onto his body. Along with a few other elemental symbols he had attached to parts of his body that could remain concealed, Naruto now have access to basic Rune magic, like healing flesh wounds and summoning fireballs.

 _"From my connection to my copy, it seemed that the Hokage is looking at your shadow clone as it prepares dinner."_ Bekka supplied after a pause.

Naruto sighed. Two weeks after he had quit school a year ago, he was called into old man Hokage's office who started grilling him about the ninja techniques he was practicing out on the training fields. It was then that Naruto realize the Hokage had been keeping watch on him discreetly. Part of him had been warmed by the fact that the old man had cared enough about him to keep a look out for him. Another part was annoyed at the fact that he was being watched without being told of it, and that it would seriously hamper his training.

Naruto had promised the Hokage that he was not going to try out the chunin ninja techniques until he was older. By the time he reached home, Bekka had came up with how the Hokage was spying on him. Apparently old man Hokage had a skill called the telescope technique in his library. It was a technique that the Hokage had created to spy upon others. The Hokage had also listed out the apparent limitation of the technique in the scroll which enabled Bekka to come up with a plan to escape the Hokage's eyes and train on their own.

Bekka had coached Naruto in learning the multiple shadow clones technique, considered a Forbidden technique which creates solid clones of one self. Bekka had computated the risk and had come to the conclusion that the possibility of Naruto dying due to the technique would only be 10% because of his large chakra reserves. Bekka had also managed to locate the Hokage's energy signature every time he used the telescope technique on Naruto.

The plan had been for Naruto to make the Hokage think the shadow clone was really Naruto, while the real Naruto would be able to escape the telescope technique by going to places where the Hokage wouldn't think of searching for him to train.

One surprising fact they had discovered when Naruto used the multiple shadow clones technique was that Bekka was also duplicated and retained the same function as the original Bekka. Bekka had quickly realized that any information the clones had received were passed onto the original when they were dispelled. Thus they ended up with the cloned Bekka and Naruto staying at home most of the day while the cloned Bekka taught Naruto New god sciences and book knowledge concerning ninja techniques, seal making and Rune magic.

When the clones dispelled at the end of the day, the real Naruto would gain all the memories of what the clone had learnt. Bekka had also asked the cloned copy of itself to keep up complex scanning and computations of it's surrounding which the cloned copy could either pass back to itself at the end of the day, or constantly transmit to Bekka the information throughout the day by maintaining a sub-wave light link between the two of them.

So for the rest of the year, the cloned Naruto had stayed at home learning 'book knowledge', only going out occasionally for 'training' so as to avoid the suspicions of the Hokage, while the real Naruto and Bekka went out to the secluded training grounds and began training in the various ninja techniques, seal making and Runes. Naruto's knowledge of technologies had improved, such that he began gathering materials to begin building some of the lower tech equipments that might come in useful.

Having mastered the basics of seal making and runes, Naruto was able to incorporate these two techniques to craft out a wooden propulsion gun that was able to shoot out pellets at great force through the engraving of several seals and symbols within it. That piece of work had taken him a month, but it had been well worth it. After all, he had no way of making the smaller parts of a true gun and thus had to come out with creative solutions through the use of seals and symbols.

 _"You will begin your schooling tomorrow. A waste of time since your ninja skill level had reached and maybe surpasses those I've scanned of chunin level."_ Bekka remarked. _"Your chakra reserves had also grown rapidly through the chakra enhancement and control exercises you've been doing for the past year. It could now be compared to most Jonin levels of reserves, though your control is somewhat lacking."_

Naruto: Hey, I'm working on my control every day! (Offended at the sore subject)

He had to work hard to get his chakra control to where it was today.

Naruto: Anyway, I've to keep up appearance, though I feel older than my eight years old.

 _"You know what exist outside this planet now, in space and all the wonders that could be accomplished with technology and rune magic."_ Bekka remarked. _"There's a 100% chance that you'll mature faster because of this knowledge."_

Naruto: I just hate the fact that I have to pretend to be stupid just because other people hate me. (says with a sigh.) Though you could always continue teaching me the Federation science while we're in class.

 _"That's a good suggestion. I'll begin to rearrange your schedule for tomorrow now."_ Bekka said as it began getting down to work.

Iruka gathered his prepared notes nervously as he walked beside Mizuki to the classroom.

Mizuki: Nervous? (laughs) Don't worry, you'll get used to teaching in no time.

Iruka: Ah yes, I hope so. (Says with a wane smile)

They walked into the classroom. The children were seated quietly in their seats, seemingly nervous as well on their first day of school.

Mizuki: You can take the role call, helps you get to know who the students are. (handed Iruka the name list for the class)

Iruka: Alright. Everyone, welcome to your first day of the academy. I am Iruka sensei and this is Mizuki sensei. I will now begin calling out your name, answer yes if the name is yours.

"…Sakura Haruno…"

"Hai!"

"Shikamaru Nara…"

"… Hai?"

Iruka: "…Naruto Uzumaki…" Iruka paused as he read out that name, his head looking up to catch sight of the little boy he had rescued so long ago.

Naruto: I am here sensei.

A Red haired boy with violet eyes, tall for his age and dressed neatly raised his hand and called out. Iruka raised an eyebrow, it seemed the little Naruto had grown into a polite young man. As he looked at Naruto's disinterested glance, Iruka realized Naruto most probably didn't remember him from that night so long ago.

Iruka: Very well, that's the last of you. We will now begin class.

Iruka said turning to nod at Mizuki. He saw Mizuki giving a small frown at Naruto before he began to tell the children to open their textbooks and began to teach them on the basics of chakra.

 **3 Weeks later, roof of the academy**

Naruto: Well Iruka sensei is a good but stern teacher. That Mizuki however is a snake. He may pretend to be nice, but I've already found him giving me misleading instructions a few times. I also overheard him calling me names. I wonder why so many people hate me.

 _"Do you wish me to provide you with an answer?"_ Bekka asked.

Naruto: Unless you can read people's minds…wait what am I saying. Ofcourse you can tell me why! Why didn't I think of this before! Bekka I need to ask you this question: Why does everyone hates me?

 _"_ _Using my Omni-knowledge, I have managed to piece together the series of events responsible for your current situation. What you are about to witness may disturb you and cause extreme emotional distress, so I advise that you allow me to keep your emotions in check in order to prevent outside discovery"_ advised Bekka

Naruto: Agree. You have my full permission to prevent me from making a scene.

 _"_ _Okay, now close your eyes"_ asked Bekka.

Naruto then set aside his bento and sat down cross legged in the shade. He then closed his eyes.

As he closed his eyes, he gasped in shock as images appeared in his head.

It was then he saw everything in history. A meteorite crashing to the ground and then becoming the God Tree feeding off the life forces of the planet, An alien woman known as Kaguya and her life, her two children Hagoromo Ōtsutsuki and Hamura Ōtsutsuki, her children sealing her into the moon, the battle between the Sage of Six Paths, his brother and the Ten-Tails, before he separated the beast's chakra into Nine, thereby giving birth to the Nine-Tailed Beasts. The Six Paths' Sons and their battle for who would be Clan Heir, with some black slime named Zetsu manipulation everything from behind the scenes. He saw the birth of both the Senju Clan and Uchiha Clan and the fight between the First Hokage and Madara Uchiha and the latter was able to control the Nine-Tails. What really caught Naruto's interest was the Uzumaki Clan. Apparently, they were the greatest masters of Sealing Jutsu and because of that they became feared. They were also recognizable because they have red hair.

He also saw a woman named Mito Uzumaki and she was married to the First Hokage. She even became the first holder of the Nine-Tails, called a Jinchuriki, shocking Naruto to the core. Before Mito died of old age, she sealed the Nine-Tails into a girl, making her the second holder. He figured was this Kushina Uzumaki. He saw how she was treated as well, but it was only because she came from another village and no one knew she was a jinchuriki. That was when she was kidnapped by the Cloud Shinboi but was saved by a boy with spiky blond hair and blue eyes like him.

The images began to change into _that_ night. The night before the Nine-Tails attack. Naruto was now shell-shocked and was in disbelief as he found out that this Minato and Kushina were in fact his own parents! The Hero of the Leave Village and Idol, the Fourth Hokage, was in fact his father!

He watched as a masked man came in after he just got born, and how said man released the Nine-Tails from his mother. And then it began, the fight, the Nine-tails rampage and then the sealing of the fox into him. He listened to his father's last words to him and was in tears.

His eyes opened in disbelief and shock as the entire truth and gravity of the situation hit him. He felt intense waves of Grief, remorse and anger swelling up inside him.

 _"_ _Your own ability to heal, as well as the strange energy signature that I have been detecting is all due to the Kyuubi. This also answers my old questions as during the sealing, somehow I was also sealed inside of you. Unlike the Kyuubi, I am not a chakra construct and my powers are taken from the source so it's sealing does not restrict me instead it bonded me to you in a more direct way."_

Naruto Why didn't you tell me? (asks in a numb tone, his mind frozen in shock)

 _"Please clarify Naruto."_ Bekka asked in a confused tone of voice.

Naruto: Why didn't you tell me about my father if you knew who he is from so long ago? (asked angrily)

 _"You never asked me to Naruto."_ Bekka said calmly. _"I am a Motherbox and although I am omniscient without your input and permission I cannot tell you he exact information unless instructed too, I can only provide you with my best answer fitting to your situations."_

Naruto: (collapses back limply on the floor as he closed his eyes, tears streaming down) My father is the Fourth Hokage and he used me as a sacrifice to contain the Kyuubi. HE'S THE REASON I WAS HATED THROUGHOUT MY LIFE! HOW CAN HE DO THIS TO ME?

 _"From what I have seen, the Fourth Hokage was ever a man to put his family and village first. According to his last thoughts, your father had wanted you to be known as the hero who saved Konoha. He had also not wanted to sacrifice another child if he could ask for his own child to carry the burden."_ Bekka said unmoved by Naruto's rage. _"He had been willing to sacrifice his own life to make sure his son and the village he loves would remain safe from the Kyuubi. Your father is not the one at fault here."_

Naruto lay for a movement in his seat, silent tears flowing down his face as he tried to regain his composure.

Naruto: What about my mother? Why did old man Hokage kept this a secret from me?

 _"Your mother Kushina Uzumaki was reported missing from the hospital not long after your father gave his life to seal the Kyuubi into you."_ Bekka reported. _"She was presumed dead, killed by enemy ninjas, her body was never found. According to the reports, your father made a lot of enemies as the Fourth Hokage, and there's many who would want to see the Namikaze clan dead. There had been no reports for me to give a conclusion as to why the current Hokage kept everything a secret from you and the whole village, but I have the answer."_

Naruto: What is it?

 _"Along with the reports on your mother, there was another one signed by the Third Hokage stating that the unnamed child of the Fourth Hokage had disappeared during the Kyuubi attack. Based on the way the Hokage feels about you, and the enemies that your father had made, I can only assume that the Hokage had wanted to protect you from the enemies of your father."_ Bekka deducted as Naruto gave an anguish sigh, his eyes squeezed tight.

 _"If news got out that you're alive after your father had died there would have been an endless string of assassination attempts made on you. Apparently from the history books of Konoha, there are records of your father slaughtering armies of enemy ninja during the Third Great Shinobi wars. Iwagakure especially suffers heavy casualty because of him and the rock ninjas bears a deep hatred for your father."_ Bekka continued her explanation.

There was silence as Naruto tried to regain his composure.

Naruto: There's nothing much I can do now. I may have the skills to protect myself, but my abilities have never been tried against powerful ninjas. After old man Hokage went through so much trouble to keep me safe, I can't ruin his efforts now, not until I've become powerful enough to really stand on my own. If he isn't going to bring this matter up to me, I've also got to pretend that I've no idea of this, after all, I can't tell him I knew all this because of you.

 _"That would be wise Naruto."_ Bekka agreed.

Naruto: My father is the Fourth Hokage, imagine that. Bekka, from now on, if you encounter any information that deals with me and my well being, inform me immediately, understand. Especially about the black slime called Zetsu and that masked man.

 _"Understood. Naruto."_ Said Bekka

 **End of Chapter One**


	2. Chapter 2: Intel Ops and the Bloodlines

**_Technologically Advanced Shinobi: A Naruto fanfic_**

 **This will be a Harem fic and I would like to Thank HandAssasinSpider-man, Diablo Ex Machina** , **VFSNAKE** , **WraithRune, MadHat886 and RebukeX7**

 **The Original story was written** **by** **WraithRune.** **I will be reposting his/her story with a few changes until the original story is finished, then I will try to continue with the story and I hope it will be good as the original considering the direction I want to go.**

 **This reality in which I am writing about is taking place in a parallel universe to the Original Naruto-verse. There are many changes in the continuity and the characters, one prominent change is that this universe is connected to the Source from the DC Reality.**

 **Since the Mother box is fused to Naruto, she can make whatever changes she can to Naruto. Remember she can manipulate both matter and energy and is more powerful than other motherboxes. She can even change his DNA to help him and that will come in handy for this chapter.**

 **Here is the new story and WARNING** **THIS STORY WILL HAVE:**

 **FOUL LANGUAGE AND CURSE WORDS.**

 **SEXUAL THEMES THAT SOME WILL FIND DEGRADING AND/OR INSULTING LIKE SHOTACON AND POSSIBLE INCEST. DO NOT READ IF YOU FIND IT INSULTING.**

 **THERE WILL BE REASONABLE AMOUNT OF BASHING AND THIS IS MOSTLY A NARUTO-CENTRIC FIC. ALL CHARACTERS EXCEPT ROMANTIC INTERESTS ARE SECONDARY CHARACTERS.**

 **POSSIBLE BAD GRAMMAR, ADULT THEMES, FAMILIAR CHARACTERS ACTING OUT OF CHARACTER AND MARY SUE.**

 **I DONT OWN THE RIGHTS TO ANY MANGA, ANIME, MARVEL, DC, VIDEO GAMES AND/OR ANIMES! ALSO NO REVIEWS OR REQUESTS.**

 **Any OC's mentioned are my own creation and property.**

 **Review in your free time and all flames will be deleted and ignored. I won't be answering questions just yet.**

 **Chapter Two: Intel Ops and the Bloodlines**

Naruto: "Bekka." Naruto said hesitantly. The knowledge of his parents now took first priority in his mind. "Can you tell me what my parents were like? Their personalities, their likes, their techniques…everything you can about them"

" _Minato Namikaze was originally an orphan, abandoned by his mother at the hospital. Due to being an orphan in a shinobi village of unknown blood, he was socially ostracized by many of his peers and fellow villagers. He entered the Academy intent on becoming a great shinobi and one day becoming Hokage in order to earn people's respect"_

Naruto immediately smiled, happy that he and his father were so similar in that respect. Even though becoming hokage was the last thing on his mind right now it was still something. 

_During his time in the academy he proved he was one of those rare geniuses who appeared once in a generation. This was further highlighted with the fact that he single handedly rescued your mother from being kidnapped by Kumo shinobi. He graduated from the Academy at the age of ten and became a student of Jiraiya, one of the three Legendary Sannins. Throughout his career, he made a name for himself and soon became known as Konoha's Yellow Flash._

 _Several of his distinctive ninja techniques include the Rasengan and the Flying Thunder God Technique. The Hiraishin is a space-time Ninjutsu which is used for instantaneous teleportation, by throwing a specialized kunai with a sealing formula he could do so. Using this technique he decimated an army of Iwa-nins._

 _Interestingly, your father was the second person to use this technique as the Nidiame Hokage Tobirama Senju was the first, but your father made the jutsu famous and created his own version of it. I have the Jutsu shikis of both versions, but I advise you to hold out on learning such a technique until your knowledge on sealing is capable enough so that you can correctly use it._

 _The other technique is the Rasengan, another famous technique"_

"Rasengan?" Naruto asked tentatively, wondering what kind of technique it was that made it his father's distinctive technique.

" _The Rasengan is the formation of a controlled ball of condensed chakra that will cause great damage to whatever it is used on. Your father created it by once observing a Tailed Beast bomb and it is the highest caliber jutsu in shape manipulation, it requires no hand signs. There were notes written by the Third Hokage stating that your father meant to further enhance the Rasengan by adding his chakra element to it, but he was never able to accomplish it before his eventual death."_ Bekka answered.

Naruto: (closes his eyes with a pained sigh) what about my mother?

" _Kushina Uzumaki was a former infamous ninja from the Land of Whirlpool. The bingo book data had commented that she had a unique ninjutsu style. She was known for creating many one of a kind ninjutsu techniques with each of them applicable to different sorts of situation."_ Bekka stated. _"Most of her ninjutsu techniques were classified as B-Rank or lower yet it was the effectiveness of the way she uses them in battle that made her known as the number one surprising ninja._

 _No particular techniques was listed in the bingo book as it seemed that Kushina's weapon was her large library of invented techniques with any techniques being used at any time. The book had highlighted that Kushina was noted for surprising and off-balancing her enemies with her quick and inventive appliance of the various techniques in battle. She was classified as an A-rank ninja."_

Naruto: Number one surprising ninja. (chukles sadly) I'd have liked to meet her.

 _"_ _Considering her reputation for being unpredictable and the fact that her body was never recovered. There may be a chance that she could still be alive."_ answered Bekka.

Naruto: No…she's dead. She has to be, I mean who would abandon their own child?

Shaking away those thoughts and focusing on the future, he made the handseal for the Shadow Clone technique. A clone of himself wearing a cloned version of Bekka appeared besides him. Naruto mentally named them N1 and B1, assigning numbers to the clones he had created. It was something he had been doing for the past year.

Naruto: Alright, I need you two to go to the administration building and scan everything over there.

N1: Done! Wait for my good news.

N1: B1, make us invisible.

He made his way towards the administration building. The real Naruto had found out during his study of New God sciences that by using Bekka to bend light around him, he could become invisible. Since one feature of Bekka was holographic projection, she was able to project light in a way that bends it around any object within Bekka's field of radius, rendering them invisible to sight.

This was another one of those 'subtle' uses of Bekka's existing functions that Bekka never bothered to tell Naruto about with the excuse that unless ordered to do so she could not do anything. Naruto had in a fit of exasperation told Bekka to be more flexible in her analyzing of what information to tell him and what not to tell him. In another words, Naruto had asked Bekka to provide him with information that provides the best possible outcomes for him.

N1 used the Body Flicker technique which allowed him to travel long distance quickly several times to arrive shortly at the administration building. The Body Flicker technique had been one of the first high level techniques Naruto had learnt, allowing him to quickly reach his secret training grounds while he left his shadow clone at his home to mislead old man Hokage.

Naruto: B1, begin scanning of the building, archive all the information scanned.

When the real Naruto had first begun using the Shadow Clone Technique, there had been some confusion over the naming of the clones. Naruto had later simply assigned numbers to represent each of the clones' names, and the clones had used the naming convention since. The clones had taken into calling the real Naruto 'Boss'.

" _Noted begin scanning."_ B1 announced.

N1 yawned, leaning against the wall of the building, watching the people go pass as he wait for S1 to finish scanning. Fifteen minutes later, S1 spoke in N1's mind.

" _N1, according to your command, you wish me to let you know of any information regarding yourself and your well being?"_ B1 asked.

N1: Ah yes, Boss did ask you to do that. (Scratching his head wondering what B1 wanted)

" _I have detected two humans working in the building who seemed to be plotting something about the Boss."_ S1 replied. _"Passing you the recorded conversation now."_

"… _Mizuki was telling us about the Kyuubi brat the other day, said that he was working hard at trying to flunk him by giving him harder questions for the tests when Iruka's not around. That brat somehow managed to did some of the questions, scraping by a pass. Mizuki swear that the fox must had a hand in this, that brat only did averagely in class, he should never have been able to attempt even a few of the chunin level questions."_ A snide female mental voice said in his head.

" _There I told you! That brat is really the fox. I don't care what The Third said about the demon being sealed in the brat, it's obvious that the fox's controlling the boy. I heard that Uzun and his gang are dropping by the brat's apartment today to spice up the fox's den a bit. They were saying that they had fixed bottle of paint with a stink component so that the stink will stay on after the paint's gone."_ Another woman's voice said maliciously

" _Tell them to be careful, The Third's protective of that brat."_ The first female cautioned.

" _The Third's an old fool, remember to misfile that mission documents I told you about, we must never let him find out about it."_ The second woman warned.

The two women go on to take about shopping and clothes with N1 listening on grimly.

N1: Alright B1, that's enough, cut off recording.

" _As you request."_ B1 said as the women's voices stopped.

N1: "B1, do you have the recordings for the previous part of their conversation?"

There something about the women's conversation making him unease.

" _Yes I do, playing now."_ B1 said.

" _This is the mission for Iruka that I told you about."_ The woman that N1 mentally labeled 'Second' said.

" _Guess being a trainee teacher must be tough, having to make ends meet by taking on extra missions."_ First said with a bit of sympathy.

" _There's no need to feel sorry for him. He's one of_ _ **them**_ _."_ Second said scornfully. _"He thinks the brat's innocent even though the Kyuubi killed his parents and left him an orphan so many years ago. Mizuki was telling us that he can't make any wrong moves against the brat while Iruka's around, apparently Iruka reports to The Third about that demon's progress in the academy every week."_

" _He has the Hokage's personal ear?"_ First asked astonished. _"He's just a chunin."_

" _From what I heard, he saved the brat from some villagers once many years ago when he's only a lowly gate guard."_ Second confided. _"The Hokage remembered such things and he promoted Iruka to assistant teacher once he got some experience under his belt. But it's obvious what the Hokage's the real motive is, he wanted someone around make sure the brat's safe. If you ask me, he's wasting good ninjas baby sitting the demon."_

" _Maybe we shouldn't mess with Iruka then, what if the Hokage finds out?"_ First said nervously.

" _Oh he wouldn't, not if you misfile it. That way no one would know that instead of a C-rank solo mission, it's actually an A-rank one."_ Second said spitefully. _"After all, he's a chunin favored by The Third, I am sure Iruka will survive somehow."_

The two women laughed.

" _You know Mizuki was telling us about the Kyuubi brat the other day…"_ The First began.

N1: Alright, cut.(anger sweeping over him) B1, finish scanning everything and let me know if any other information against the Boss, Iruka sensei and the Hokage's well being come up."

" _Proceeding with request now."_ S1 said agreeably.

N1 waited in angry silence, there would be hell to pay once he passed the information to the real Naruto.

Iruka sensei just finished the class on basic math when N1 passed Naruto all the information he learnt. Sica was most probably receiving the archive of mission reports that S1 had scanned as well.

When Naruto opened his eyes, his eyes blazed in anger at the sight of Mizuki walking into the classroom as he took over the class from Iruka.

Naruto: _Well now I know that Mizuki's really against me._ (things angrily). _And I need to find a way to make sure Iruka's sensei going to be safe._

Naruto went over N1's memories. Apparently, after being informed by B1 of what happened, N1 had ordered B1 to report back if it detected any more conversations that go against the well being of himself, Iruka sensei and old man Hokage. B1 had detected two more conversations about several administration officers covering up certain information to lead the Hokage astray.

One of the conversations in particular resolved around another administrative officer who was unhappy with the way the Hokage always protects the 'fox brat', causing him to vindictively sabotage some of the important administration files.

Naruto frowned, it seemed that old man Hokage and Iruka sensei were coming down under a lot of fire for supporting him, if only he could find some way to help them… As he thought, an idea creep into his mind and his eyes widened. He looked at Sica wrapped around his right wrist and grinned. Yes, it would work, he **would** make it work! Because the Hokage and now Iruka sensei had become his precious people, and he would do his best to protect them from harm.

 **2 weeks later, Hokage's office**

Sarutobi frowned as he looked down at the sealed message in his hand. For the past two weeks he had been receiving intelligence reports about the going-ons around the village. These reports were delivered to his home at intervals during the two weeks. He had the Anbu questioned the delivery boys, but all of them had a different description of the man who hire their delivery services, suggesting that the informer is hiding under an illusion.

The problem was that the information in the scrolls was always very accurate, too accurate for Sarutobi to just look a gift horse in the mouth. The first scroll had enabled Sarutobi to save Iruka, a chunin academy teacher from coming to serious injuries in a dangerous A-rank mission. Sarutobi had also discovered several leaks and informants from the civilian political factions operating in the ninja administrative building with the next subsequent scrolls.

The scope of the information began to grow larger with each scroll, and it seemed that the informant began expanding his area of operations in Konaha. Sarutobi managed to apprehend a spy from rock village who was operating in Konoha under the guise of a toy merchant. Information regarding the under table deals of several high ranking merchants in Konoha were also sent to Sarutobi and exposed in the various scrolls. It had prompted Sarutobi to send a few military police to keep an eye on those merchants, waiting for them to make a wrong move so that the police could apprehend them.

Sarutobi began to wonder what the intentions of this mysterious benefactor were. He wasn't as naïve as to believe that this informant who was most probably a powerful and skilled infiltration ninja, would provide these information for free. Sarutobi began to go through all the information sent by the scrolls to current date and could only find one common link. All the information provided the mysterious informant were information that could have caused harm to the citizens of Konoha if nothing was done. In particular, plots against the Hokage or any of the Hokage's favored ninjas were particularly highlighted in the scrolls.

Sarutobi had questioned his intelligence operatives, but all had replied that the scrolls were not of their work. Jiaraya who was the main source of intelligence news outside of Konoha would not have operated in such a style. Konoha was known for powerful ninjas versed in the ninja arts, but it was never known for powerful _infiltration_ agents, there were precious few in Konoha who could gather so much information in such a wide area, within such a short time.

In the end, Sarutobi still had not been able to reach a conclusion of who the informant was. He had however assigned one Anbu to constantly keep watch of his house in case a new scroll arrived. If a new scroll did arrive at the Sarutobi clan house, the Anbu was ordered to deliver the scroll to him at once.

With time, as the scrolls kept arriving, Sarutobi became well informed of events outside his knowledge. His hold on the village had also strengthened. Sarutobi had also come to acknowledge that maybe there was some ninja out there with the will of fire, keeping watch over Konoha.

Those Anbus who were in the know began calling this mysterious informant, _'The Eye of Konoha'_.

 _"One of the merchants has sent a huge bribe to Kuma, the civilian council member in charge of Konoha's banking system."_ Bekka announced as Naruto was having his dinner.

Naruto nodded as he swallowed the eel he had cooked. "Did the Watcher clones receive the information?"

" _Checking the sub light link… Yes, Watcher B1 has received the information, Watcher N1 is in the process of copying it."_ Bekka reported.

Naruto nodded with a grin. When he had begun the intelligence operations, he had not known that there was so much dirt hidden in Konoha. The urge to protect old man Hokage and Iruka sensei was what prompted his foray into information gathering. But as time went on, he found that he had a lot of fun with this whole intelligence gathering business. It was therapeutic to know about the plans of someone who was planning to harm you or those that you care about and then turn those plans against them.

Several villagers who were planning to vandalize his apartment had been caught in the act and were fined by the military police. When another group had tried to wreak havoc in Naruto's home out of retaliation, they were caught in the act as well after Naruto sent a scroll informing the Hokage about the event beforehand.

There are now cloned Narutos stationed beside the administrative building, the ninja academy, the financial sector and the Hokage tower. There were also ten more Naruto clones patrolling the streets of Konoha gathering information as they made their way across the village. Naruto would create clones every morning to begin the information gathering process. These Naruto clones would use the cloned Bekkas attached to them to scan the respective areas. At first, Naruto had only targeted information that brought harm to Iuka sensei or the Hokage. He had later broadened the scope to include the protection of the whole village.

Sure most of the civilians in the village treated him badly. But old man Hokage would be troubled if any part of the village came into trouble. Naruto also did not want to become like those villagers that had treated him badly. After all, if he came into information that could harm the village and not inform the Hokage, he would just be like those narrowed minded villagers he hated.

To avoid detection, each of the clones remained invisible through the use of the cloned Bekkas' holographic projection abilities. The real Bekka had cautioned Naruto that there was a clan in Konoha who could see through objects. Bekka had no idea if those clan members could detect the invisible Naruto clones, however all the cloned Bekkas were reminded to constantly keep a look out for the clan members by scanning the area around them for their presence. According to the real Bekka, the Hyuga clan members were easy to detect due to a unique genetic marker that all of them possessed. This genetic marker was what gave them their bloodline abilities called the Byakugan.

Once night arrived, Naruto would create a new batch of clones. These clones would take over the positions of the clones from the morning. The morning clones would then dispel themselves passing all their information to Naruto and Bekka whereupon Naruto would then shift through the information to see if they had missed out anything important before retiring for the night. When morning arrived, Naruto would then replace the night clones with the morning clones.

He had also created two special clones during the day and night patrols that hide out in one of the training ground armed with scrolls and brushes. These clones were assigned the names of Watcher S1, Watcher N1 and Dispatch S1, Dispatch N1 respectively. All information from the various spy clone units were transmitted from their cloned Sicas to Watcher S1 via the sub light link. Watcher N1 would then retrieve the information from Watcher S1 and write them on the scrolls.

Depending on the seriousness of the information, the Dispatch N1 would then be sent to the Sarutobi clan house straight away, or they would wait until morning or night, before the next clone shift takes over. Dispatch S1 would project an image of some random delivery boy over Dispatch N1, thus misleading the ANBU watching over the Sarutobi house.

Tonight, Naruto had decided to expand his information collection a bit further. He had sent a clone to the ANBU building to see if there was any dirt to be had there. The clone had reported that it had reached its position an hour ago, after which it had begun scanning the area.

 _"_ _Naruto, I have come across certain information which may offer a new opportunity. It is in regards of using the Gene manipulator function_ "said Bekka.

Naruto: Gene Manipulator? Explain Bekka.

 _"_ _The Gene Manipulator is a function of mine created to supplement me in aiding any intelligence agents. Coalition under New Genesis' protection contains many different species of sentient creatures besides humans. The Gene Manipulator comes in handy if an intelligence agent needs to infiltrate another planet that is not of his race or species."_ said Bekka.

 _"_ _My database contains the gene maps for most of the sentient species in the Universe. By inputting the gene maps into the Gene Manipulator, the intelligence agent can use the machine to change into the species he is trying to infiltrate, with the infiltrator possessing all the traits and physical structure of the species. Basically the whole DNA structure of the intelligence agent is changed to allow for better infiltration._

 _The Gene Manipulator could also heal genetic disease, but one thing to note is that it does not heal viral or bacteria infection. If you're poisoned, changing your DNA structure wouldn't help unless you're changing into a species with immunity to that poison. Your overall mass would not change as well when you undergo gene mutation."_

Naruto: (blinked at the explanations) I understand how it's going to be useful for the New Gods where humanoids aren't the only sentient race. But how is it useful to me right now? On my own planet?

" _Your planet has certain humans possessing genetic quarks that you call bloodlines. I am able to scan and isolate the gene that causes these bloodline limits, since they are unique genetic markers in the normal human structure."_ Bekka explained. _"I could then pass the gene map to the Gene Manipulator and use it to give you that bloodline limit."_

Naruto: A bloodline limit. (interested) What bloodline limit have you scanned?

" _Currently I've only detected and identified the Byakugan bloodlimit, during the time when you pointed out one of the Hyuga clan members to me."_ Bekka replied.

Naruto: Aren't the characteristic of the Byakugan bloodline white eyes? (pauses) It would be pretty obvious to everyone that something happened if I started walking around with white eyes. Aren't there other bloodline limits you have detected?

" _I've detected a few other bloodline limits through your journey around the village everyday, but unfortunately since I do not have a name to go with the people who bears the genetic markers, I am unable to deduct what type of bloodline limits belong to those genetic markers. It would not be advisable for me to pass them to you."_ Bekka explained _"However, I may have a suggestion._

 _Based on an old Anbu report, Orochimaru, student of the Third Hokage, used to conduct vile research on implantation of the Wood Release gene belonging to the First Hokage on human subjects. His methods were unethical and result in many deaths. His lab was shut down and he was chased out of the village when the Third Hokage found out about it_." Bekka replied. _"I currently have the location of that lab, and according to the ANBU reports, the labs were simply shut down and sealed under the most powerful seal known to the Third Hokage._

 _The gene solutions and various equipments which might still bear the Wood Release gene were never destroyed but simply sealed within. I suggest creating a clone to scan out that area for the Wood Release gene marker. The Wood Release is a powerful bloodline and is not outwardly visible physically which should be suitable for you."_

Naruto then made the handseals for the Shadow Clone technique as a clone of himself puffed into existence beside him.

"N16, you know what to do." Naruto said eyeing the clone. "Dispel yourself after S16 have gotten the Wood Release genetic marker."

Naruto sat down as his clone dispelled and information of the Wood Release gene was transmitted to Bekka. He was surprised that Bekka also reported to him that she had also scanned several other DNA. One was from an unknown clan, that according to orichimaru's notes could passively collect and use Nature Chakra, he was using them to go into what he called "Sage mode", the others were the Kurama clan's Yin release gene, Mito Uzumaki's DNA which according to his notes could use Chakra chains and lastly the Kaguya Clan's bloodline limit the Dead bone pulse which was capable of creating undefeatable taijutsu masters.

According to Orochimaru's notes, a combination of these DNA could create what he called a perfect body. He originally wanted immortality so this was a sure shot way in getting it, however his research was cut short when the Sandiame caught up to him.

Naruto decided that since all these bloodlines could not be visibly noticed and would not change him much physically, he would go through with it especially if it meant regaining more of his Mother's heritage from Mito Uzumaki.

In order to make assimilation easier and to prevent complications, Bekka manifested a small green pellet. It appeared infront of Naruto on the floor in a flash of light.

 _"_ _The pellet is actually made up of nano-bots specially programmed to change your genetic structure. You'll spend at most five hours in a feverish state as the gene mutation occurs , changing your body to accommodate the new gene materials. I will be able to relieve some of your pain during the process through the Rune magic engraved on me, and there's a possibility that your regeneration abilities will also aid in the process. After the mutation process ends, you'll come into possession the new abilities."_ said Bekka.

Naruto reached out and took the pellet in his hand.

Naruto: So I just eat it? (eyes the pellet)

" _Yes, I would suggest you do so laying on your bed. The pellet would knock you out during the gene mutation process."_ Bekka suggested. _" While you are indisposed I will also be doing some modifications to myself, in order to make me more combat ready and to work well with your new powers"_

Naruto nodded, setting everything aside before lying on his bed. He held the pellet above his mouth and dropped it in, swallowing it.

A sense of vertigo hit him, and then he knew nothing more.

He woke up… in a sewer, crawling with vines of greenery that was rapidly spreading.

"What the hell happened?" Naruto muttered as he got up, water splashing around him. "Bekka?"

There was no response.

"Bekka! Bekka where are you?" Naruto asked frantically as he searched the water and the sewer around him. Apart from the growing vines and the rock walls of the sewer, Bekka was nowhere to be found.

Naruto: What could have happened? (Asks in confusion)

He remembered eating the pellet that was supposed to give him the new bloodlines, he remembered fainting, and then he had woken up here. Naruto was contemplating searching the sewer around him again when a loud roar of pain reverted through the cold and damp tunnels. Naruto flinched, the sound seemed to be coming from the other end of the sewer.

Naruto felt unbelievably exposed. Sure he was well versed in a lot of D and C-rank techniques with even a few B-rank techniques. He could most probably do well in a fight against some chunin or even a few low level jonin. But now that he was facing some unknown element alone, Naruto felt the beginnings of fear. He had come to rely on Sica to provide him with advice about what to do for most of his life. He wasn't sure if he could make the right decisions if left on his own.

The roar sounded again, like the cry of some wild and dangerous wild animal. Naruto pondered if he should walk deeper into the sewer to find out what was going on. He looked around himself. He had no idea where he was, a brick wall signaling the end of the sewer was behind him, and the only way out was to walk deeper into the sewer and hope for the best. Naruto took a deep breath to fortify himself as he took the first step deeper into the sewer. His senses were on high alert. He was a ninja trained by Bekka, he would not let those teachings go to waste.

After minutes of walking and the constant roaring of the wild beast which was becoming weaker with every moment, Naruto found himself at another dead end. This time, there was a giant cage draping with green leafy vines crawling all over the bars of the cage. Within the cage, Naruto saw with horrified eyes the battered body of a giant nine tailed fox that was bind to the floor of the sewer by several large roots.

Vicious red chakra was emitting from the fox, spreading out of the cage. But when they touched the vines crawling all over the bars of the cage, the demonic red chakra changed to a tide of cool green tingled with tendrils of brown. These waves of green brown chakra washed over Naruto, giving him the feeling of rich clean growth and sensation of being in the forest of Konoha. As Naruto basked in the calming green brown chakra, more vines and roots burst out of the ground around him, spreading to cover the whole walls of the sewer.

The eyes of the trapped fox opened and glared at Naruto.

Naruto: You! (hisses) You are the boy! What have you done to me?

Naruto stared at it, nearly taking a step back at the killing intent the fox let out, before the green brown chakra bolstered his defense, allowing him to match the fox's stare. Naruto's eyes flickered briefly to the paper seal on the cage door and then looked at the fox.

Naruto: I assumed you are the Kyuubi that's supposed to be inside me. (Sounding calm) I've been wondering what you really looked like. I wasn't expecting the greatest of the tailed beasts looking like this.

Kyuubi roared in anger as Naruto pointed derisively at the roots binding it.

Kyuubi: I am the most powerful of the tailed beast and I will find my way out of whatever you've done. (snarls) And when I escape from here, you'll be the first to be eaten by me!

Naruto: Please, like that's going to scare me." (says with a sniff, trying to cover the deep seated fear in the pits of his stomach) Anyway I've done nothing, except to give myself the Wood Release bloodline.

Kyuubi: The Wood Release bloodline! (gapes at Naruto and looks horrified) You brat! What have you done!

Naruto flinched at the angry roar from the Kyuubi this time as it struggled in the roots that kept it trapped. An enormous wave of red chakra pulsed out of the cage, and the vines could not totally purify some of it, causing some of the red chakra to be mixed in with the green brown chakra.

Naruto shuddered painfully as the red chakra washed over him and he…

" _I see you've awaken Naruto."_ Bekka's voice sounded in his head. _"The gene mutation was a success. You now possess the First Hokage's Wood Release bloodline as well as the other bloodlines."_

Naruto: I'm back in my room. (says with relief)

He opened his eyes, getting up and looking around his room to confirm that he's really not in the sewer anymore. His eyes widened at the plants that had grew in a fan shape around his bed. Most of them seemed to be attached to the floors and the bed.

Naruto: What the hell happened here?

" _I am unsure, though it might be a side effect of your bloodlines. I've also detected some abnormality during the mutation process."_ Bekka continued. _"During the mutation, great amounts of the energy that I have classified as the Kyuubi's chakra was emitted from your body in a controlled manner._

 _The Kyuubi's chakra however disappeared after only five minutes into the mutation, and I sensed a new kind of energy signature that I've never felt before emitting from you. Shortly thereafter, the plants began to grow around you. My deduction is that the Wood Release and the Sage bloodlines converts the Kyuubi's chakra into a new type of chakra that allows the rapid and forced growth of plants."_

Naruto: Then that means my dream is actually real. (In part awe and part horror)

" _Dream?"_ Bekka asked.

Naruto: Yes well, I had a dream about the Kyuubi just now.… the Kyuubi was bond onto the floor by these giant roots and most of the red chakra coming out of the cage was converted into greenish brown chakra.

" _Analyzing data… I propose a hypothesis which might be 95% correct in light of the new information."_ Bekka offered. _"What you just had was a psychic connection to Kyuubi. It seemed that the addition of the Wood Release and Sage bloodlines in your body might have allowed you the ability to control the chakra of the Kyuubi from this moment on. According to the data about the Wood Release ability, the First Hokage was able to use that ability to successfully suppress and control the tailed beasts during the First Shinobi War. You may have gained that similar ability."_

Naruto: So that means that I might be able to control the Kyuubi's chakra at will now? (amazed)

" _Maybe not right away. However it might be wise to add learning Wood Release techniques into your schedule. I would also to run some sub routines and tests while you train and with time I might be able to come up with ways for you to tap into the Kyuubi's chakra."_ Bekka added. _"The extra data will also enable me to come up with various strategies for ways you could put your abilities to greater use in battle"_

Naruto: (grins) Alright! That's going to be so cool! Too bad I've to go to the academy during the day now, or we'll have more time training.

" _Actually Naruto, if I may suggest something, you might want to consider sending a clone to attend the ninja academy while you train during the day."_ Bekka suggested. _"The cloned Naruto could use his Bekka to generate solid Holographic shields that will protect the clone from any physical damage._

 _The holographic shields will not be able to hold out under strong attacks, but they should be enough to provide more time for your clone to escape. Considering that the regular academy training spar is against children who do not even possess 10% of your current ninja skills, you should be quite safe."_

Naruto: Good suggestion Bekka. Though I may not want to become the Hokage now, I do want to become strong enough so that I can protect myself and those that I care about. And when I am one day able to travel to New Genesis, I'll show them that though the people from my planet might be primitive, we're descended from one of the strongest races out there! The race of ninjas!

 **End of Chapter 2**

 **A/N: Please review. Flames will be deleted. Keep this story alive please.**

 **On the note of the story, Naruto now has the power to use all 5 elemental affinities, Wood Release, Sage chakra, Adamantine chains, powerfull and realistic illusions and the Dead bone pulse. Combine this with the Super-Motherbox fused into him and he is already godlike.**


End file.
